diff --git a/CHANGELOG.md b/CHANGELOG.md index 341074b816..e20ea1a9d2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,7 @@ ### Maintenance and fixes - Make `arviz.data.generate_dims_coords` handle `dims` and `default_dims` consistently ([2395](https://github.com/arviz-devs/arviz/pull/2395)) - Only emit a warning for custom groups in `InferenceData` when explicitly requested ([2401](https://github.com/arviz-devs/arviz/pull/2401)) +- Update `method="sd"` of `mcse` to not use normality assumption ([2167](https://github.com/arviz-devs/arviz/pull/2167)) ### Documentation diff --git a/arviz/stats/diagnostics.py b/arviz/stats/diagnostics.py index 290803ae69..e7dba32bab 100644 --- a/arviz/stats/diagnostics.py +++ b/arviz/stats/diagnostics.py @@ -744,8 +744,8 @@ def _ess_sd(ary, relative=False): ary = np.asarray(ary) if _not_valid(ary, shape_kwargs=dict(min_draws=4, min_chains=1)): return np.nan - ary = _split_chains(ary) - return min(_ess(ary, relative=relative), _ess(ary**2, relative=relative)) + ary = (ary - ary.mean()) ** 2 + return _ess(_split_chains(ary), relative=relative) def _ess_quantile(ary, prob, relative=False): @@ -838,13 +838,15 @@ def _mcse_sd(ary): ary = np.asarray(ary) if _not_valid(ary, shape_kwargs=dict(min_draws=4, min_chains=1)): return np.nan - ess = _ess_sd(ary) + sims_c2 = (ary - ary.mean()) ** 2 + ess = _ess_mean(sims_c2) + evar = (sims_c2).mean() + varvar = ((sims_c2**2).mean() - evar**2) / ess + varsd = varvar / evar / 4 if _numba_flag: - sd = float(_sqrt(svar(np.ravel(ary), ddof=1), np.zeros(1)).item()) + mcse_sd_value = float(_sqrt(np.ravel(varsd), np.zeros(1))) else: - sd = np.std(ary, ddof=1) - fac_mcse_sd = np.sqrt(np.exp(1) * (1 - 1 / ess) ** (ess - 1) - 1) - mcse_sd_value = sd * fac_mcse_sd + mcse_sd_value = np.sqrt(varsd) return mcse_sd_value @@ -973,19 +975,21 @@ def _multichain_statistics(ary, focus="mean"): # ess mean ess_mean_value = _ess_mean(ary) - # ess sd - ess_sd_value = _ess_sd(ary) - # mcse_mean - sd = np.std(ary, ddof=1) - mcse_mean_value = sd / np.sqrt(ess_mean_value) + sims_c2 = (ary - ary.mean()) ** 2 + sims_c2_sum = sims_c2.sum() + var = sims_c2_sum / (sims_c2.size - 1) + mcse_mean_value = np.sqrt(var / ess_mean_value) # ess bulk ess_bulk_value = _ess(z_split) # mcse_sd - fac_mcse_sd = np.sqrt(np.exp(1) * (1 - 1 / ess_sd_value) ** (ess_sd_value - 1) - 1) - mcse_sd_value = sd * fac_mcse_sd + evar = sims_c2_sum / sims_c2.size + ess_mean_sims = _ess_mean(sims_c2) + varvar = ((sims_c2**2).mean() - evar**2) / ess_mean_sims + varsd = varvar / evar / 4 + mcse_sd_value = np.sqrt(varsd) return ( mcse_mean_value, diff --git a/arviz/tests/base_tests/test_diagnostics.py b/arviz/tests/base_tests/test_diagnostics.py index f30865d824..69e2946a86 100644 --- a/arviz/tests/base_tests/test_diagnostics.py +++ b/arviz/tests/base_tests/test_diagnostics.py @@ -120,10 +120,11 @@ def test_deterministic(self): ``` Reference file: - Created: 2020-08-31 - System: Ubuntu 18.04.5 LTS - R version 4.0.2 (2020-06-22) - posterior 0.1.2 + Created: 2024-12-20 + System: Ubuntu 24.04.1 LTS + R version 4.4.2 (2024-10-31) + posterior version from https://github.com/stan-dev/posterior/pull/388 + (after release 1.6.0 but before the fixes in the PR were released). """ # download input files here = os.path.dirname(os.path.abspath(__file__)) diff --git a/arviz/tests/saved_models/stan_diagnostics/reference_posterior.csv b/arviz/tests/saved_models/stan_diagnostics/reference_posterior.csv index 52059ba5ad..86eca35f29 100644 --- a/arviz/tests/saved_models/stan_diagnostics/reference_posterior.csv +++ b/arviz/tests/saved_models/stan_diagnostics/reference_posterior.csv @@ -1,49 +1,49 @@ "","rhat_rank","rhat_raw","ess_bulk","ess_tail","ess_mean","ess_sd","ess_median","ess_raw","ess_quantile01","ess_quantile10","ess_quantile30","mcse_mean","mcse_sd","mcse_median","mcse_quantile01","mcse_quantile10","mcse_quantile30" -"d",1.00780272388603,1.0004168232094,465.136513484671,349.135270438316,467.84472286415,467.84472286415,311.806319792457,467.367576858138,1500.2193689464,754.211496074801,354.746981701936,0.00265985849234941,0.00188197776671187,0.005242,0.00812199999999999,0.003997,0.00375200000000001 -"sigmasq_delta",1.01090196780102,1.00035874354121,73.249623982678,48.5806371372426,134.497570910906,134.497570910906,132.049677080929,138.627800274732,33.1982442776445,63.6980562732759,98.6290985074029,0.00114848510125919,0.000813869235009484,0.00095392,0.0003001,0.00044662,0.00058668 -"mu.1",1.00731450966132,0.999545827128633,1231.30913527034,1119.63456276454,1189.5912192317,1137.76545007779,811.795584886629,1171.62891354699,1030.60309993778,465.95223908163,635.768730056618,0.0125124382036461,0.00904921314805709,0.022465,0.02589,0.0285949999999999,0.0175350000000001 -"mu.2",1.00332752771857,1.00046552033653,558.783738495551,920.913340029631,569.193418116839,569.193418116839,560.847913565582,543.893011358525,1250.00943663727,715.745937098207,603.702320409943,0.0100753323647403,0.00712798968840261,0.012035,0.0344149999999999,0.0169700000000002,0.0116750000000001 -"mu.3",1.00400884522485,1.00119273844036,545.006145537412,721.191572843273,525.001599973821,524.853529459804,409.25009203697,519.896707667091,980.123379207968,597.010589383932,776.855700473939,0.012221584083923,0.00864799158514802,0.0182549999999999,0.0148200000000001,0.0200100000000001,0.015765 -"mu.4",1.00992230528499,1.00088653210741,582.054899011997,475.118727680651,572.691571673006,572.691571673006,453.404375352865,590.532677591646,1150.49950736189,1061.12497686928,297.464682466101,0.00338150237488137,0.00239230207501219,0.00423499999999999,0.00789000000000017,0.0046250000000001,0.00692500000000007 -"mu.5",1.00733922911401,1.00017537414794,754.786642573516,1073.96515350853,763.910100475586,763.910100475586,762.522622136922,764.757297566194,1601.95897581453,823.748224208616,602.971885735321,0.00535619470645841,0.0037888485986391,0.00728499999999999,0.01271,0.0105449999999998,0.00721499999999997 -"mu.6",1.0063264651477,1.00019046380718,681.62514557434,841.509646646211,710.977179062472,710.977179062472,469.426815292446,690.219361038972,496.664104993923,854.423772463052,799.11107396604,0.0128934361623842,0.00912077887401999,0.02196,0.0800150000000002,0.0284499999999999,0.015415 -"mu.7",1.0009508247325,1.00226228815332,338.501572250893,798.174111097497,338.298033186001,336.342131243366,271.172024542225,326.217452597384,925.997070900362,842.297594532647,322.156375656936,0.00461535071570276,0.00327586361996432,0.00647500000000001,0.00655499999999998,0.00410999999999995,0.00627499999999992 -"mu.8",1.0090643975564,0.999538833472528,500.370209497559,578.884594887594,493.348188663339,493.348188663339,313.922618265292,505.50985231336,1386.39640838638,640.804896232492,697.131902186388,0.00532227304880204,0.00376564253357891,0.00929000000000002,0.0093049999999999,0.0109100000000002,0.00605499999999992 -"mu.9",1.01019493017765,0.999603164368487,340.342755003858,946.607791310506,333.492896973282,317.156110862577,484.326477329234,356.445106502136,1562.99962092251,56.5180669671026,220.186644019022,0.00778879135503874,0.00565277446712757,0.00825999999999993,0.0133449999999999,0.0254349999999999,0.014645 -"mu.10",1.00075487572724,0.999511473112951,583.991419920615,471.41183217468,588.283043747639,588.283043747639,477.481294770335,590.14928532837,799.772115109561,906.418393458689,311.515150979097,0.00276260856418602,0.00195442858016026,0.00405000000000011,0.011425,0.00260499999999997,0.00502000000000002 -"mu.11",1.00595414640273,1.00237422670742,635.15097952383,800.479933058152,665.620410175752,660.540967368931,519.624529420413,655.71371952012,945.861386301234,586.20076491672,408.369416259054,0.00431255652753725,0.00306249301583716,0.00705500000000003,0.0158449999999999,0.01007,0.0102799999999998 -"mu.12",1.0047268539977,1.00514527883668,496.929163495088,531.044721860628,504.262711368638,498.71991830265,319.158390701001,480.727694997398,1853.86082845226,572.398861171123,317.880247530293,0.0057037756397616,0.0040579031206402,0.00858499999999995,0.0151549999999999,0.01154,0.00814000000000004 -"mu.13",1.008945349242,1.0056573986565,183.23984965215,350.35095755959,187.049324363394,187.049324363394,475.166782427048,178.745879678592,719.678538769825,371.680213864137,532.208029969556,0.0173131687638012,0.0122613993208749,0.00905,0.0248349999999999,0.0225550000000001,0.013755 -"mu.14",1.01304235232272,0.999571875876497,146.455619305836,905.20577806428,156.913168025411,156.913168025411,326.757781606977,184.871406789517,1501.15708995927,275.031545588726,379.47949263356,0.0112582926739193,0.00797565952859592,0.00992499999999996,0.00940499999999989,0.012775,0.00852999999999993 -"mu.15",1.00166475852766,1.00098644134086,647.052787106276,631.753828191276,650.018161664313,650.018161664313,658.62198403898,643.855640478447,836.543429989515,760.283671777858,375.926738510082,0.0060179931852768,0.00425727465663249,0.00807999999999998,0.0173800000000001,0.0116149999999999,0.00492999999999999 -"mu.16",1.00740317948224,1.00853464974225,499.036519568152,746.05300433263,501.454892472435,487.572301780466,485.396752318049,472.13048627122,1341.97413184728,277.102847934913,609.721215668554,0.00640986388102947,0.00459928387444533,0.00609499999999996,0.014005,0.0172800000000001,0.00823499999999999 -"mu.17",1.00235785729279,1.00079863526808,568.525190685684,577.67526711659,570.160744519767,570.160744519767,549.959891120856,563.848255834083,1431.69084406391,747.739233140895,581.929203983128,0.00753372166353053,0.00532987316400548,0.00883,0.02302,0.0112099999999999,0.011695 -"mu.18",1.0058815147689,0.999605048059416,542.537401212283,553.368100868642,550.366452404361,550.366452404361,433.167272775349,584.744508829451,1341.05872361933,720.895449370801,422.716253311391,0.0122763089002585,0.00868526574623527,0.01478,0.0384899999999999,0.0162549999999999,0.02017 -"mu.19",1.00414368524188,1.00060208238245,449.416857063488,739.485184107347,446.219468477619,446.219468477619,345.725868771874,449.137074366437,1561.55711641925,544.69861487889,419.996836681418,0.0160809134566196,0.0113783637269282,0.02644,0.0399750000000001,0.0198449999999999,0.02633 -"mu.20",1.00303319392542,1.00045657842583,429.352356666043,667.698241600053,408.218014375817,391.527783333572,416.536296772659,400.23475139616,1563.70741553559,133.612813080646,279.606683576796,0.00693974335849805,0.00501437741069646,0.00812000000000002,0.015245,0.012025,0.010345 -"mu.21",1.00975536911073,1.01022808966214,374.47529790908,470.815645795366,364.204306828113,362.753916792411,336.118912328005,339.216837731465,1055.53653994431,585.531004662949,181.680640103669,0.00699623341543813,0.00496095516705718,0.00904500000000019,0.0112399999999999,0.00910499999999992,0.0165649999999999 -"mu.22",1.00294755213814,0.999600478698527,674.597258384371,600.678471867714,678.699385312521,676.074215660601,324.316517855015,680.605387522155,908.437133488286,764.541352392027,383.852018821601,0.00533742583176886,0.00378308286397595,0.0127699999999999,0.010505,0.007185,0.00717499999999993 -"delta.1",1.00193273557651,1.00110042421068,1172.74856393641,974.786547170996,1419.23404652728,730.513415976935,649.830820193221,1410.38271694321,977.529406338044,782.300515662223,668.284695026047,0.0038676938490309,0.00381349766950887,0.0048955,0.0203195,0.00914400000000001,0.00684599999999999 -"delta.2",1.00439696727112,0.999671764127513,757.273755729389,1041.21641448256,841.741917392082,727.465871898432,440.437505212779,836.017025076283,910.440957531096,819.510207777999,444.090052381873,0.004732095521024,0.00360077411885722,0.0056435,0.0389715,0.013379,0.00763449999999999 -"delta.3",1.0048779262348,0.999733784057189,854.667318035899,601.21846326955,881.923285826473,626.48555548841,667.795651854425,871.389790934645,1030.78267333512,610.820032214856,543.056438051934,0.00483645532470362,0.00405951695827326,0.00615350000000001,0.0424825,0.0080035,0.00698349999999998 -"delta.4",1.00178244152549,0.999578735499239,933.614899067375,750.167856320662,960.420142222955,851.271396005864,466.804294420143,952.265093307421,1562.99962092251,808.248888293026,848.385826906282,0.00286776827314079,0.00215463906107671,0.00450449999999999,0.016153,0.00641250000000002,0.00339400000000001 -"delta.5",1.01081774716755,1.00241813072529,586.411691467462,943.409653768766,610.921485388949,610.921485388949,493.500353919725,620.944209858451,1396.11137524087,958.339509742365,773.928892663521,0.00509922346905432,0.00360741832991934,0.008062,0.020229,0.007526,0.00504300000000002 -"delta.6",1.00190020811646,1.00213136770008,933.591422341378,680.772965157487,917.641844958604,554.312744743189,466.105251245502,869.978957461908,1019.34979665739,615.944560171407,464.449517690915,0.00467404005100357,0.00425466396526783,0.00564049999999999,0.042385,0.0136695,0.00843949999999999 -"delta.7",1.00412724855361,1.00244365868817,229.195505938696,203.70063395052,239.599032907495,239.599032907495,258.226892482532,235.167900306928,1298.99528753311,469.228350866314,335.674635373719,0.00738452488138673,0.00522801720999206,0.00690850000000001,0.00962150000000001,0.011208,0.00955349999999999 -"delta.8",1.01302686669844,0.999978104471402,767.371699778806,1069.01390989025,773.726493231428,773.726493231428,524.725055273805,788.520229384147,1617.62037766705,1228.32563592793,321.895527707361,0.00418005595173392,0.00295686083398161,0.0074535,0.0110275,0.00659949999999998,0.0072275 -"delta.9",1.00240486051678,0.999686448177722,967.147813834466,805.14293480976,921.332318713367,788.822348916106,714.971441907896,911.348066015492,1181.60609792208,988.399569707274,453.575392453051,0.00390437482860046,0.00298480324159655,0.00506200000000001,0.0135795,0.00882050000000001,0.00756899999999999 -"delta.10",1.01148346905793,1.00079092738233,221.58398760916,512.070682182092,227.340028184212,227.340028184212,321.202034626446,234.227618555189,1552.55702598724,1158.43349854518,502.709517349779,0.00558111846776516,0.0039515209209377,0.006744,0.010841,0.00319900000000001,0.00472249999999999 -"delta.11",1.00436479181684,0.999546010444357,865.224447923886,936.150395054657,900.81898633316,900.81898633316,420.212037985204,909.208813980858,1856.30870029447,998.186312144878,432.595765534901,0.00353200967338314,0.00249831707951844,0.005305,0.0114425,0.00684750000000001,0.00582550000000001 -"delta.12",1.0051455786984,1.00090228472677,746.592500353552,819.359175324269,748.477550571627,748.477550571627,464.352491232897,748.709658864382,1622.75285471028,1154.40505296934,436.170801499081,0.00438862230801511,0.00310443466209018,0.005106,0.00893000000000002,0.00667599999999999,0.003271 -"delta.13",1.00712064755481,1.00136237270726,783.642427498241,702.762955320348,727.365240511934,563.476817227379,590.519739539685,722.362255781916,891.110531194617,594.203121864699,517.190497501428,0.00513748338041085,0.00412951090024318,0.005607,0.068738,0.0169845,0.00620400000000002 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